Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

    This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

    A few questions so far:

    1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
    -Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

    2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
    -when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions

    Comment


    • #17
      Sorry clicked too fast...

      Sorry I should add that so far I have done this:
      >WT<-"C1"
      > mut<-c("C2","C3","C4","C5","C6")

      Originally posted by gareth.lim View Post
      My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

      This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

      A few questions so far:

      1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
      -Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

      2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
      -when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      52 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X